Wastewater discharges into fluvial ecosystems represent a significant and continuous source of fine particles and nutrients that can severely modify stream community composition and functionality. Depending on both wastewater and stream features (e.g., nutrient removal treatments and stream dilution capacity), the ecological effects can be more or less severe. To determine how hyporheic habitat and hyporheos are affected, we analysed eight Mediterranean streams both upstream and downstream of a wastewater effluent. The results demonstrated that environmental factors associated with clogging, such as the quantity of fine particulate and organic matter in sediment, were magnified downstream of the wastewater inputs. Likewise, dissolved nutrients also increased but depended to a greater extent on the presence of a wastewater treatment plant and on the nitrogen and phosphorus removal treatments. The hyporheic invertebrates were more affected by clogging than by eutrophication. Both richness and diversity parameters were negatively correlated with clogging features but were not correlated with eutrophication. The most affected taxa were Macrocrustaceans, Hydrachnidia and several insect species, which decreased or were not detected downstream of the effluents. On the contrary, other taxa such as Naididae (Oligochaeta), Orthocladiinae (Chironomidae) and Potamopyrgus antipodarum (Gastropoda) benefited from the wastewater inputs.